## A Winter Short Course on Statistical Mechanics for Molecular Simulations (2015)

Computational molecular simulations have become invaluable tools for research in physics, chemistry, biology, and material sciences. In this short course of 7 lectures, Prof. Yuan-Chung Cheng will provide a general overview of statistical mechanics and algorithms useful in simulating complex molecular systems. Issues in molecular modeling and fundamental rigorous theories will be emphasized, and the content will consist of developments of methods that have broad applications in physical chemistry. Practical issues will be discussed in this course, but they will not be the focus here. Most of the course content is based on Frenkel and Smit’s book.

This set of lectures are open to all participants. **All students interested in the topics are welcome to participate in the lectures.**

This webpage will be updated often to provide links to my lecture notes and online resources. If you have any questions or suggestions, please shoot me an email at yuanchung@ntu.edu.tw or leave a reply below.

### Tentative Schedule & Topics

Due to the timing of the Chinese new year in the winter break, this version of the winter short course will be presented in mostly two weeks. Each meeting will be about 2 hours, and the lectures will focus on covering the principle theoretical ideas in each topic listed in the following:

- Statistical Mechanics (1/22, 1:30PM) (lecture note, lecture slides).
- Molecular modeling and interactions (2/2, 1:30PM) (lecture note, lecture slides).

2013 Chemistry Nobel Lectures: Martin Karplus, Michael Levitt, Arieh Warshel - Monte Carlo simulations (2/4, 1:30PM) (lecture note).
- Molecular dynamics simulations (2/6, 1:30PM) (lecture note).

Related papers:

McCammon’s review paper

Tuckerman’s Nose-Hoover chain paper - Free energy calculations (2/9, 1:30PM) (lecture note, lecture slides).

Related papers:

Good Practices in Free-Energy Calculations

Practical Aspects of Free-Energy Calculations: A Review

Replica-exchange MD

Weighted histogram analysis method

Metadynamics - Non-equilibrium phenomena — stochastic dynamics (2/11, 1:30PM) (lecture note, lecture slides).
- Non-equilibrium phenomena — fluctuation-dissipation (2/13, 1:30PM) (lecture note, lecture slides).

### Location

All lectures will be held at Room 121 @ NTU Chemistry Building.

### Reference Materials

This set of lectures will be based on Frenkel and Smit’s book:

Understanding Molecular Simulation, Second Edition: From Algorithms to Applications by Daan Frenkel and Berend Smit

Publisher: Academic Press

http://www.amazon.com/Understanding-Molecular-Simulation-Second-Edition/dp/0122673514

### Prerequisites

Attendants should have been familiar with notions of thermodynamics and classical mechanics. The followings are some good references: